I'm sorry that my answer is not a Perl based but if the only thing you want to do is sort the lines based on the first column here is a simpler solution for you: 
cat data-file.txt |sed 's/^Cluster//'|sort -k1 -n|sed 's/^\([0-9]\+\)/
+Cluster\1/' > sorted-data.txt

[download]
Here is the output with pasted a few times your test data: 
$ cat dd |sed 's/^Cluster//'|sort -k1 -n|sed 's/^\([0-9]\+\)/Cluster\1
+/'| cut -c 1-20
Cluster5        SP_1003(con
Cluster5        SP_1003(con
Cluster5        SP_1003(con
Cluster6        SP_0917(pil
Cluster6        SP_0917(pil
Cluster6        SP_0917(pil
Cluster7                spr_1379(A
Cluster7                spr_1379(A
Cluster7                spr_1379(A
Cluster8                spr_0324(T
Cluster8                spr_0324(T
Cluster8                spr_0324(T
Cluster9        SP_0733(hyp
Cluster9        SP_0733(hyp
Cluster9        SP_0733(hyp
Cluster10       SP_0042(co
Cluster10       SP_0042(co
Cluster10       SP_0042(co

[download]
I hope I have helped.
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In reply to Re: split function problem by hackman
in thread split function problem by $new_guy

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